Oligonucleotides are known to be able to bind to double-helical DNA in the major groove of the helix, thereby forming a triple helix structure. The code for binding to form a triple helix (hereinafter referred to as the triple helix code) does not follow the same code as that for the binding of two single-stranded polynucleotides to form a double helix. The code for triple helix formation is set forth, for example, in Moser, H. E. and Dervan, P. B., Science (1987) 238: 645-650, and in Coohey, M., et al., Science (1988) 241:456-459. According to this code, isomorphous base triplets (T-A-T and C-G-C.sup.+) can be formed between any homopurine-homopyrimidine duplex and a corresponding, third, homopyrimidine strand. Since the rules limit the sequences which can form a triple helix it would be desirable to obtain oligonucleotides which can bind to form a triple helix in one portion of a duplex and cross over the groove in the double helix to bind to another portion of the duplex, thereby extending the portion of the duplex which can be "read." Such oligonucleotides would allow for identification and location of unique portions of double-helical DNA similar to the manner in which unique portions of single-stranded DNA are identified and located by single-stranded oligonucleotides.
The invention provides oligonucleotides which have inverted polarities for at least two regions of the oligonucleotide, thereby allowing the respective inverted polarity segments to read complementary strands of a double-helical duplex. By "inverted polarity" is meant that the oligonucleotide contains tandem sequences which have opposite polarity, i.e., one having polarity 5'.fwdarw.3' followed by another with polarity 3'.fwdarw.5', or vice versa. This implies that these sequences are joined by linkages which can be thought of as effectively a 3'--3' internucleotide junction, (however the linkage is accomplished), or effectively a 5'--5' internucleotide junction. Such oligomers have been suggested as by-products of reactions to obtain cyclic oligonucleotides by Capobianco, M. L. et al., Nucleic Acids Res (1990) 18: 2661-2669.